"A fierce firefight ensued and is still ongoing," Lieutenant Colonel Edgard Arevalo , a navy spokesman, told AFP news agency.
He said the Abu Sayyaf unit was led by Albader Parad and Abu Pula, two senior commanders of the group thought to be holding Vagni.
Two other aid workers seized along with Vagni were released separately in April.
Ronaldo Puno, the interior secretary, said last week that Vagni was alive, but many weeks in the harsh tropical jungle was taking its toll, as he is said to be suffering from a hernia.
Puno also said that efforts to recover Vagni were being slowed by landmines planted by the Abu Sayyaf fighters.
US and Philippine intelligence agencies say the Abu Sayyaf has links to Jemaah Islamiyah, a regional group believed to be fighting for a pan-Asian Islamic state, and is also said to have had links with al-Qaeda.
The group has been blamed for the 2004 bombing of a ferry near Manila Bay that killed at least 100 people.